My speed at the MAF Heart Rate has slowed during the Two-Week Test. Am I losing fitness?

It's unlikely. At all times, the body uses two different fuels: fat and sugar. At lower intensities (such as below the MAF MAF) the body uses a greater percentage of fats. However, a small percentage of its energy still comes from sugar.

During the Two-Week Test, the reduction in dietary sugars and carbohydrates means that the body has less available sugar than it usually does. It can’t supply the sugar that it usually burns under the MAF HR. This means that while the fat-burning systems are fully fueled, the sugar-burning systems aren’t. The body is forced  to rely almost exclusively on fats during the Two-Week Test.

The observed reduction in power, then, has nothing to do with a loss of fitness. When working under the MAF HR, the body is usually running both of its engines: the fat-burning engine is going at maximum, and the sugar-burning engine is putting out a small amount of energy. During the Two-Week Test, the fat-burning engine is still at maximum, but the sugar-burning engine is almost completely turned off. Both engines are still as powerful—it’s just that only one of them is working.

This is a very positive thing. By shutting off the sugar-burning engine and relying completely on the fat-burning engine for 2 weeks, the body now has a much bigger reason to both develop the fat-burning engine and make absolutely sure that all of its various organs and systems can be powered by that fat-burning engine. This is “fat-adaptation.”

In other words, it is because the body loses a bit of speed during the Two-Week Test (and not despite it), that we know it is receiving a powerful stimulus to become more fat-adapted.